He netted the Cobblers' all-important 79th minute winner, a goal which dented the play-off hopes of his former club.
His strike was one of the few highlights of a match which never really hit any great heights.
There was little in the way of cohesive play from either side in the opening exchanges with no chances of note being created in the first 20 minutes.
The only real talking point during this phase was an early penalty claim by Boston when Julian Joachim tumbled under a challenge from Luke Chambers, but referee Neil Swarbrick waved play on.
Boston finally gave the crowd something to cheer in the 26th minute when Joachim went on a surging 40-yard dash. But his left-foot shot at the end of a lung-bursting run flew straight at Lee Harper.
The home side enjoyed by far the greater territorial advantage, notably forcing eight corners in the first half hour, but with no end product.
Northampton's first opportunity took 37 minutes to arrive. Ex-Boston man Andy Kirk crossed from the right, but in turn Jason Crowe and then Martin Smith had shots blocked by keeper Michels Kuipers.
Boston had a chance to break the deadlock on 50 minutes when Lawrie Dudfield burst clear, only to be denied by a great tackle from Chambers as he prepared to shoot. And moments later, Jamie Clarke drilled wide as Boston pressed again.
In the 59th minute Simon Rusk got in behind the Town defence but drilled straight at Harper after being picked out by Clarke.
The visitors still found it hard to impress and Kuipers was only troubled by a long-range shot from Crowe in the 66th minute.
But the Cobblers finally got their act together and took a 79th minute lead when Johnson steered in a cross from the left by Smith.
Boston tried to respond, but failed to find a way through a visiting rearguard in which Chambers and Sean Dyche were commanding figures.